November 15, 2022
Gene transcription — the elaborate process that our cells use to read genetic information stored in DNA – was long thought to be turned on only when certain regulatory factors traveled to specific DNA sequences. In a new study published in Genes & Development, Mittal et al., 2022, discovered that a subset of genes has their transcription regulatory factors and cofactors already in place, but in a latent state. With the appropriate signals, these “poised” genes become highly active.
The authors calculated the DNA-bound preinitiation complex/TBP-associated factor (PIC/TAF) ratio at all yeast genes and identified two major classes. The first, and largest, group provides basic “housekeeping” functions and are usually “on” at very low levels all the time (i.e., “constitutive”). The second class, the “inducible” genes, has a whole entourage of “poised” proteins assembled nearby which provides a guiding hand to transcription machinery when triggered by environmental signals, resulting in high levels of “induced” transcription.
Using CRISPR-Cas9 mediated protein depletion/degradation and gene knockout techniques, Mittal et al. removed parts of the SAGA and TFIID cofactors to systematically examine the role they play in regulating the above gene classes. They discovered that the constitutive class largely depended on TFIID, whereas the inducible genes required both SAGA and TFIID, suggesting an integrated pathway of PIC assembly at inducible genes. If true, such a possibility would be different from previous models where the two cofactors were thought to engage in somewhat distinct mechanisms of PIC assembly.
The authors further examined the above results and were surprised to find that at the inducible promoters, SAGA stabilized Taf1p (and thus TFIID) which helped in a rapid and robust transcription initiation of these genes upon acute environmental changes.
In addition, Mittal et al. also removed gene-specific transcription factors (TFs) to address how these factors recruited TBP upon sensing changes in environmental signals. They showed that TFs such as Hsf1p and associated cofactors were already bound to gene promoters prior to induction, instead of traveling to cognate sites upon induction. These cofactors, thus, lend a helping hand in recruiting TBP and the associated machinery at the induced genes.
Lastly, Mittal et al. removed Gcn5p and DUB subunits of SAGA to examine the effect on histone acetylation and ubiquitylation, respectively. They showed that global histone acetylation and ubiquitylation levels require active Gcn5 and the deubiquitination (DUB) activities, suggesting a SAGA independent moiety contributing towards maintaining total cellular acetylated and ubiquitylated histone pools.
Contributed by Chitvan Mittal.
Categories: Research Spotlight
May 27, 2022
Eukaryotic transcription is most often initiated by RNA polymerase II (RNAPII) and regulated by several factors, including epigenetic factors, histone modification, DNA methylation, and non-coding antisense transcripts. Non-coding antisense transcripts, produced from the strand opposite to the sense strand, use transcription interference (TI) to regulate gene expression. TI is a phenomenon where one transcription activity negatively impacts the other in cis. One such example is when transcription of long non-coding RNAs (lncRNAs) overlaps with coding gene promoters, causing repression of that gene. Antisense transcripts are involved in several biological processes and show dysregulation in different diseases; however, the mechanisms underlying the antisense mediated transcription interference (AMTI) are not well understood.
An exciting study by Soudet J et al. in Nucleic Acid Res has identified new components in budding yeast to be involved in AMTI. The authors highlight a strong connection between HIR histone chaperone complex binding and antisense transcription in context with SAGA or TFIID-dependent gene regulation. Likewise, the study shows that induction of antisense transcription influences HIR binding, nucleosome repositioning, and (de novo) histone deposition.
Furthermore, data show that antisense transcription into promoters at SAGA-dependent genes restricts the access of the transcription factor binding sites (TBSs) and transcription factors (TFs) by closing the promoter nucleosome depleted regions (NDRs) with nucleosomes, thus repressing the genes. When antisense elongation begins, nucleosomes are randomly lost from the promoters, and chromatin has a chance to reopen again before new nucleosomes are incorporated. In the absence of HIR complex, the promoters stay open and upregulate the SAGA-dependent genes.
The study confirms that SAGA-dependent genes are associated with higher HIR binding and antisense transcription into promoters. Interestingly, TFIID-dependent genes do not show the same effect even in the presence of high antisense transcription levels. Although SAGA and TFIID-dependent gene classes share a high level of antisense transcription as a common feature, the authors propose that genes can interchange these classes when the balance between TF binding and nucleosome incorporation is changed.
Thus, the study sheds light on the mechanism of the antisense mediated transcription interference and emphasizes the role of the HIR histone chaperone complex in gene regulation.
Categories: Research Spotlight